Reduced Individual Matrices From Group Regions

Reduces individual matrices using the average reduced group profile.

Description

Usage example

regions_nomenclature:            /my/path/share/brainvisa-share-4.6/nomenclature/translation/nomenclature_desikan_freesurfer.txt

study_name:                      studyA  

region:                          lh.inferiorparietal

subjects_group:                  /my/path/brainvisa_db/subjects/group_analysis/g1/g1_group.xml

complete_individual_matrices:    /my/path/brainvisa_db/subjects/001/diffusion/default_acquisition/default_analysis/default_tracking_session/connectivity_parcellation
                                 /avg/studyA/lh.inferiorparietal/matrix/001_studyA_lh.inferiorparietal_complete_matrix_smooth3.0_20to500mm.imas'

filtered_reduced_group_profile:  /my/path/brainvisa_db/subjects/group_analysis/g1/connectivity_clustering/avg/studyA/lh.inferiorparietal/smooth3.0
                                 /g1_avg_studyA_lh.inferiorparietal_filtered_watershed_20to500mm.gii

average_mesh:                    /my/path/freesurfer_db/group_analysis/average_mesh_group/average_brain/averagebrain.white.gii

regions_parcellation:            '/my/path/freesurfer_db/group_analysis/average_mesh_group/average_brain/bh.annot.averagebrain.gii'

normalize:                       True

intersubject_reduced_matrces:    '/my/path/brainvisa_dbsubjects/group_analysis/g1/connectivity_clustering/avg/studyA/lh.inferiorparietal/smooth3.0
                                 /g1_avg_studyA_lh.inferiorparietal_001_reduced_matrix_20to500mm.nii.gz'

Parameters

regions_nomenclature: Nomenclature ROIs File ( input )

Nomenclature of the cortical parcellation used to partition the study.
Example : Freesurfer Desikan_Killiany Atlas

study_name: String ( input )

General name of the study, links to corresponding study data in output_database to retrieve profiles computed during the individual processing.

region: OpenChoice ( input )

The study region based on regions_nomenclature file.

subjects_group: Group definition ( input )

The XML file corresponding to the subjects group.

complete_individual_matrices: ListOf( Connectivity Matrix ) ( input )

List of the complete individual matrices (cortical region vertices, cortical surface vertices) of each subject of the group.

filtered_reduced_group_profile: Connectivity ROI Texture ( input )

Group profile after watershed computing and elimination of low connectivity basins.

average_mesh: White Mesh ( input )

Freesurfer average white mesh of a group of subjects.

regions_parcellation: ListOf( ROI Texture ) ( input )

Cortical parcellation used to partition the study.
Example : Freesurfer Desikan_Killiany Atlas (?h.aparc.annot).

Implications of the choice of the method on the regions_parcellation parameter:
(1) averaged approach: the regions_parcellation parameter must be a file representing the average parcellation of the group of subjects.
(2) concatenated approach: the regions_parcellation parameter must be a list of files, each representing the individual parcellation of a subject of the group.

normalize: Boolean ( input )

This check box allows to normalize each reduced matrix of the list intersubject_reduced_matrices.

erase_smoothed_matrix: Boolean ( input )

intersubject_reduced_matrices: ListOf( Connectivity Matrix ) ( output )

Each subject obtains a reduced matrix from its individual complete matrix. There are as many reduced matrices as input subjects.

Technical information

Toolbox : Constellation

User level : 2

Identifier : constel_reduced_individual_matrices_from_group_regions

File name : brainvisa/toolboxes/constellation/processes/group_pipeline/tools/constel_reduced_individual_matrices_from_group_regions.py

Supported file formats :

regions_nomenclature :

Text file, Text file

subjects_group :

XML, XML

complete_individual_matrices :

Sparse Matrix, Sparse Matrix

filtered_reduced_group_profile :

GIFTI file, GIFTI file, Texture

average_mesh :

GIFTI file, GIFTI file, MESH mesh, MNI OBJ mesh, PLY mesh, TRI mesh

regions_parcellation :

GIFTI file, GIFTI file, Texture

intersubject_reduced_matrices :

gz compressed NIFTI-1 image, GIS image, NIFTI-1 image, gz compressed NIFTI-1 image